A Glitch in the System
by The Writing Archer
Summary: Change one thing, and you change everything. That's the basis for what is called chaos theory or the butterfly effect, and if something as small as a butterfly flapping its wings can change the world, then what would happen if Emiya Shirou's childhood was spent living on the run from Magi before the boy found his way into the Underground? Interesting is at least a given.


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 **A Glitch in the System**

 **Book 1: A life on the Run**

 **Prologue**

* * *

 _Fate, for all the talk around it that it can't be changed, is such a fickle notion._

 _Even as a child Shirou knew that. He had become intimately familiar with it about a year after being saved and moving into the Emiya Estate with his adoptive father, Emiya Kiritsugu._

 _After all, the Emiya Estate was supposed to have been the place where he grew up. It was supposed to be the place where he lived together with Kiritsugu, the place he was supposed to return to every day after school, the place where he, hopefully, would one day be taught Magecraft by his father._

 _That was supposed to have been his 'Fate' for the next decade or so._

 _That changed the second he and his father had been forced to abandon the Emiya Estate in a hurry, leaving all that he knew behind in a split second decision that more than likely saved both their lives._

 _All because of the mercurial whims of a Magus._

 _Oh, and all the enemies his father had made when he was still the Magus Killer. Can't forget about that._

* * *

It was a dark and cold night, and only the warmth provided by the campfire and the tiny body snuggled into his side kept Emiya Kiritsugu from shivering.

He was currently sitting on a log in some god forsaken forest somewhere in Japan in the middle of nowhere. His adopted son was sprawled up against him, eyes closed and completely dead to the world, sleeping peacefully.

How had it come to this?

Hah! What a stupid question. Kiritsugu smiled bitterly to himself. It was all his fault, his actions bringing misfortune to both himself and everyone he cared about as he just did whatever he wanted to do, never thinking about the consequences that might arise from his actions.

As per usual.

It had happened less than nine hours ago. He had just returned from his latest failed attempt at retrieving his daughter from the Einzbern (his fourth attempt thus far), and had been quiet and moody as a result. His adopted son, Shirou, had picked up on this and had acted accordingly.

First he had made dinner for them both, a skill he had picked up on his own as Kiritsugu himself couldn't cook worth a damn, and in spite of being only seven years old Shirou had proven to be a natural cook.

And while they ate a rather delightful dinner of rice, fish and several spices, Shirou offered his constant quiet support, giving him the chance to wind down, just waiting for the moment they could have a relaxed conversation over some Japanese tea like they always did whenever he came back from his trips from Germany.

But before they could do that a letter of thick parchment had arrived. A letter which bore the family crest of the Einzbern, and the message it had carried was damning.

One which permanently made the prospect of sharing stories over tea at home an impossibility.

Kiritsugu sighed and prodded with a stick at the fire, idly stroked his son's bright red hair with a calloused hand, his free arm slung around the child. The boy really was a blessing, in more ways then one. The child was kind, considerate and so damn helpful all the time... If it wasn't for Shirou and his constant bright presence in his life Kiritsugu was sure he would have long since gone off the deep end.

It just made him feel even guiltier then he already did.

Shirou had saved him from drowning in his own despair and guilt in the disastrous aftermath of the Fourth Holy Grail War, and how does he repay his son?

With a target on his back.

Kiritsugu shuffled a little closer to the campfire, feeding the remains of the stick into the flames. The night was getting progressively colder.

To be fair, even Kiritsugu had not expected how cruel the head of the Einzbern family could be. Merely keeping his daughter from him clearly wasn't good enough revenge for Old Man Acht. Apparently, even though he had once again been soundly rebuffed from retrieving his daughter by the Bounded Fields surrounding the Einzbern castle, his latest attempt had either frightened or annoyed Acht enough to finally take active measures against him instead of just shutting him out and declaring him persona non grata.

And he did so by announcing his current place of residence to practically every major organization that in anyway dealt with the supernatural/hidden side of the world.

Anyone who even had the slightest inkling of Kiritsugu's past knew what that meant.

He was almost universally hated in the Magus community. As a freelancer he had already accrued the general disdain of most traditional Magi who considered Magecraft only as a field of study, but the _work_ he had done during his time as a mercenary, that which earned him to title of Magus Killer, made him a reviled man by many.

The clue was in his title. Many a Magus had died at the end of the barrel of his gun or by one of his many traps and tricks, a fact which had earned him quite a few enemies, a lot of which would be willing to go to almost any length to get a piece of him.

The Archibald family in particular came to mind. The head of the Archibald family had been a contestant in the Fourth Holy Grail War, and it had been by Kiritsugu's hand that the man had been terminated. He might not have pulled the trigger himself, but it had been by Kiritsugu's actions and manipulations that the man had died.

Even worse. The way he had done it had totaled the Archibald family Magic Crest.

Oh. And he had caused the death of the man's accomplice during the War who just happened to be the man's fiance.

As such, he was pretty sure any remaining Archibalds would salivate at the chance to make him suffer.

Kiritsugu squeezed his eyes shut.

But informing anyone that might have an axe to grind with him where he lived had not been enough for Acht. As an extra incentive the man had placed a massive bounty on the former Magus Killer's head. The letter he had received from the man had included a short message of why and what the old man had done, a few scathing remarks, and a copy of the bounty transcript. The sheer number of zeros in the payment being offered for anyone that succeeded in killing him had been enough to make his head spin.

That hadn't been the worst of it though.

Kiritsugu drew Shirou a little closer to him, tightening his hold on him, as if he was scared the boy might disappear if he let go of him.

If he had succeeded in retrieving his daughter (and found a way to make sure no one would come after them to get her back) he would never have looked back to the Einzbern again. So long as his daughter was still whole and healthy if and when he got her back he would never meddle in their affairs again. In fact, he would have more then happily forgotten all about the Einzbern.

Let bygones be bygones and all that.

His free hand dug into the bark of the log he and his son were sitting on, fingernails piercing completely through it.

But placing a bounty on his innocent son's head as well... that he could and would never, _ever_ forgive.

He knew Magi could be cruel. In fact, he couldn't help but know it, having seen and dealt with the worst of them, but that really was beyond the pale.

Forcefully calming himself down, Kiritsugu took stock of his situation.

He and Shirou had been forced to abandon the Emiya Estate in a hurry with little more then the clothes on their backs. As no one knew of their current location they should be safe for at least a little while. He was certain that Magi who were determined enough to find them would eventually do so if they invested enough time and resources.

But only if they staid put long enough for them to do so.

Moving around was going to be paramount in the future for their continued safety.

Looking at the red headed boy snoozing against his side, Kiritsugu felt guilt gnaw at his heart. A life on the run, constantly moving around, was not appropriate for a child.

He should know. Kiritsugu's father had been the recipient of a Sealing Designation by the Mage Association because of his research into vampirism, and had dragged his son, a little kid at the time, all over the world in a mad bid to evade the Association's Enforcers.

Kiritsugu shook away the memories that thought brought to mind - _Shirley, Natalia, father_ \- and refocused on the situation at hand.

Money was not an issue, as he had more then enough hidden away in more than two dozen accounts all over the world, one of the few minor benefits he had gotten out of his former life as the notorious Magus Killer.

Most importantly...

Kiritsugu briefly glanced at a large suitcase sitting innocuously in the warm glow of the fire.

...he still had his weapons.

The thought of the several kinds of guns and ammunition housed in that innocent looking suitcase, especially his trusty Thompson Contender and his Origin Bullets, filled him equally with relieve and weariness.

Relieve because the tools were invaluable for his and his son's protection, and weariness because he had hoped to never have to rely on them again.

Kiritsugu grimaced and coughed briefly as his heart throbbed with a familiar pain. He placed a hand on his chest, probing for the deep, constant ache in his flesh, bones, and even his Circuits.

There was a problem though.

The curse placed on him by the spirit housed in the Holy Grail, Angra Mainyu, was killing him. Ever since the end of the Fourth Holy Grail War his flesh grew weaker, his bones becoming more and more brittle as time wore on, and his Circuits were slowly but surely deteriorating at an alarming rate.

His time was short. There was no denying that.

He gave himself three, maybe four years at most, before he died.

And when he died there would be no one to protect Shirou from the many enemies he had made as the Magus Killer, or any unscrupulous Magi (which, unfortunately, made up the fast majority of Magi) looking to make a quick buck.

Shirou murmured something in his sleep, and the Magus tightened his hold on the boy a little bit more.

If it were an option, he would have no doubt hidden Shirou away. Changing the child's appearance with the aid of one of the few Magi that owed him a favor, he would in spite of his own wants have parted ways with the child after crafting him a new identity and a new life to settle into while he went on the run.

That was, considering the current situation and his own impending death, the best option he could think of.

Unfortunately, that option was closed to him by virtue of the kind of people that were hunting them. Magi could be thorough and relentless in pursuit of their goals, and if one were to couple that with the resources they had and the variety of methods, both mundane and Thaumaturgical alike, they could employ to locate people...

They'd find him. No matter what. No matter what clever scheme he used or how well crafted the child's disguise, they would find him and then kill his son.

After all, the only reason why they had been left alone so far was because Shirou had been a non-factor in the Magus community, while the fast majority of Magi had believed him to be dead, yet another casualty in the meat grinder that was the Holy Grail war.

No, now that Acht had blown open the secret that he still lived finding refuge in obscurity was now no longer possible. Either for him, or for Shirou.

For better or for worse, he had to remain by Shirou's side to protect him. He might be the cause for the danger his son was in, but if Kiritsugu were to leave him on his own now without some form of protection he might as well sign the child's own death warrant himself.

But the same problem remained. He couldn't remain by his son's side. His death was imminent. Angra Mainyu's curse assured that.

Kiritsugu took a deep breath, and then let out an explosive sigh.

There really was nothing for it. Considering that all other options were few and their margins of success small, there was only one sensible path in regards to his son that he could take.

If he could not shield Shirou from the world himself... then the only logical action he could take was to teach his son how to protect himself instead.

Kiritsugu chuckled bitterly. Shirou had been bugging him to teach him Thaumaturgy practically from the second he had informed him that he was a Magus. Kiritsugu had been adamantly against it. The life of a Magus was characterized by pain, suffering and death. Honing one's Craft was as libel to kill you as it was to produce results. If it were at all possible he would have preferred his son to have nothing to do with the world of Magi, and that included studying the dangerous art known as Thaumaturgy.

That was no longer possible now that the world of Magi had come knocking on their door and then chased them from their home on its own accord, and that necessitated that he grant Shirou's earnest wish to learn magic. However much it pained him, however much he didn't want his son to become a Magus, the choice was no longer his.

Closing his eyes and leaning back, the Magus Killer removed his lingering doubts and steeled his resolve.

He would get his son started on the basics as soon as possible, but first they needed to get out of the country. Japan was no longer safe for them anymore. Any other country, ideally one that was removed as far as possible from any heavy presence of Magi, would be much more preferred.

After throwing off any would be pursuers from their trail, buying them some time, he would need to procure the necessary materials to start Shirou's education in Thaumaturgy. To do that Shirou's Magic Circuits needed to be opened and then he would have to perform the preparations required for the ritual that would identify what his son's Origin and Element are.

But Magecraft wouldn't be the only thing he be would teaching Shirou. Trap making, tactics, stamina and physical fitness, even how to handle modern weaponry and technology. Every little thing that had given him an edge over other more traditional Magi. All that he knew and had employed in combat as a mercenary, down to the very philosophy he swore by as the Magus Killer, he would impart onto the Shirou to maximize his chances for survival.

Kiritsugu's heart clenched painfully as he came to that resolution.

Cruel.

His conscious whispered poisonous words into his mind. There was no other or better way to describe it. What he was going to do to his son for his wellbeing was going to be cruel. He was going to _have_ to be cruel to teach Shirou all about combat, magic and what it meant to be a Magus Killer.

To safeguard Shirou's life and give him the greatest chance at even having a future, he was going to have to be cruel and strip him of his childhood innocence.

Just like how his own had been stripped away by cruel circumstances and uncaring Magi.

"Hmm," Shirou groaned against Kiritsugu's side as he woke up. His son looked blearily up at him, and blinked. "Dad, what's wrong?" the child asked with a small yawn at the end. "You seem kind of mad... wait, why are you crying?"

Was he crying? Kiritsugu raised a hand and touched the wetness streaming steadily from his eyes.

Kiritsugu didn't cry often. In the pursuit of his ideal, he had hardened his heart to the point that he was more like a machine acting on preordained function. He had effectively shut out all emotions to such an extent that he could barely feel them at times when he was still foolishly pursuing his impossible dream. The times that he had cried could be counted on one hand without the thumb, and each and every one of those times had emotionally scarred him in some way he would never recover from.

The last time he had cried was when he had pulled Shirou from the flames he himself had caused when he rejected the Holy Grail. That was the only time he had cried tears of joy in his life, simply because he had found a life in that hellish blaze that he could save.

Those tears, and the near dead boy had found lying on the burned ground, had acted like a balm to his soul.

And now he had destroyed that boy's life all over again. Two times in a row. Not even mentioning what he was going to do to that boy to make sure he lived.

No wonder he was crying. Now he only felt cold and empty on the inside.

"Dad, don't cry!" Shirou now sat up straight and started to futilely try to wipe away Kiritsugu's tears. "What's wrong? Come on, tell me what's wrong. If there's anything I can do to help you, dad, you just need to say it."

Kiritsugu felt a flicker of warmth return to him at Shirou's words, and an even deeper guilt taking root at what he had done to this incredibly kind child. Shirou's eyes widened as he was suddenly pulled to Kiritsugu, who embraced him as tight as he could and spoke haltingly to his son, the words almost inaudible in the crackle of the campfire.

"I will not ask you to forgive for what I have done to you and what I am going to do to you, Shirou," Kiritsugu hiccupped, "But if you really want to make me feel better, could you please promise me one thing?"

Shirou, while confused by his father's actions and words, nonetheless nodded his head after a moment's hesitation. "Of course, dad."

Tightening his hold a little more, Kiritsugu made an impassioned plea to his son, "Promise me that you will do everything in your power, no matter what it takes or what you'll have to do, and no matter what may happen in the future or what dangers you may face that you will live a long and happy life."

Shirou was silent for a long moment. He did not know why his father would ask something like that from him. The boy knew that he and his father had been chased from their home, though he did not know by whom and why, and he was smart enough to realize that they were in danger even now. But he had faith that an awesome Magus like his father would be able to keep them save. He was sure that everything would be fine so long as they stuck together.

That was the line of reasoning that was going through Shirou's mind, based on nothing more than the absolute trust in his father and his partial understanding of the situation, unaware as he was of the curse that ensured that the man that had saved his life did not have long te live.

Nonetheless, if making such a promise would make Kiritsugu stop crying and feel better...

Shirou separated a little from Kiritsugu, remaining in his arms but pushing back far enough to look his father in the eyes, and smiled brightly. "No problem, dad. I promise I will grow up to be happy and strong, even if I have to keep looking for happiness for all my life. I so swear!"

* * *

 _And so, the Fate of the boy named Emiya Shirou was irreversibly changed._

 _Not just because of the mercurial whims of a Magus, a reason of which he was aware, but also because a different promise had been made between a loving father and the son that admired him than had been intended by Fate's grand design, an eventuality that even the Swirl of the Root could not have predicted or contemplated._

 _In other words, it was a single glitch in the system that brought forth a series of events that could not and should not have happened. An impossibility that would, in the end, change the world's intended course, with no one being able to tell anymore what was going to happen next._

 _Now isn't that interesting?_

* * *

 **And? What do you guys think? I would love to hear each and everyone's opinion in the reviews.**

 **While I have been visiting this website for many years, it was only recently that I bothered to make an account of my own and start posting my own work. I chose to make a crossover between Fate and Undertale because I love the sheer range of possibilities that the Fate franchise offers (characters, abilities, the well-developed system of magic and reality) and the beautiful and touching (with sometimes rather hilarious undertones) story of Undertale.**

 **Of course, the fact that both franchises really hit me in the feels when I was going through them might have something to do with that, as well.**

 **I hope that I don't disappoint, and, I'll say it again; please review. I'm dying to hear what my readers think of my work.**


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